Posts about Life Science

Ocean Exploration – Live Feed and Highlights

Nautilus Live provides a live view of the E/V Nautilus as it explores the ocean studying biology, geology, archeology, and more. The site also includes highlights such as this video of a siphonophore.

Siphonophores are actually made up of numerous animals even though they look like one animal. These amazing colonial organisms are made up up many smaller animals called zooids, and can be found floating around the pelagic zone in ocean basins. The Portugese Man O’ War is a famous siphonophore.

Each zooid is an individual, but their integration with each other is so strong, the colony attains the character of one large organism. Indeed, most of the zooids are so specialized, they lack the ability to survive on their own.

Related: Giant Star Fish and More in AntarcticaHydromedusae, Siphonophora, Cnidarians, Ctenophores (what are jellyfish?)Macropinna Microstoma: Fish with a Transparent HeadLarge Crabs Invading Antarctic as Waters Warm

Here is another video from Nautilus, showing a large dumbo octopus:

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Nutrition and Digestion in Horses

Unlike cattle which have several stomachs (and there own interesting digestion system), horses have only one stomach. Like cattle their natural diet is grass. With feed provided by people, horses can run into issues they don’t experience from their natural diet. Fresh grass is fibrous and slows down digestion. If feed is used the feeding should be spread out several times during the day, due to the horses digestive system.

image of the digestive system of a horse

image via eXtention. The next 4 paragraphs are slightly edited quotes from the link.

The small intestine is the main site of digestion and absorption of protein, energy, vitamins and minerals.

The cecum is located after the small intestine of a horse and it functions much like the rumen of a cow (as a fermentative vat housing microbes which aid digestion). These microbes break down nutrient sources that would otherwise be unavailable to the horse.

The cecum and colon house bacterial, protozoal and fungal populations which function in microbial digestion of feed material in the digestive tract. Many different products of microbial digestion are absorbed by the horse.

Among other benefits, incorporating long-stem forage into rations increases particle size of ingested matter, thus slowing rate of passage. It also increases dry matter intake, thus stimulating water intake.

Nutrients and Common Feed Sources for Horses from the extension service (USA land grant universities)

Carbohydrates provide the majority of a horse’s energy. Non-structural carbohydrates, such as starch and glucose from grains and gums and pectins from fiber, are readily utilized as energy sources for the horse. The enzyme amylase breaks down non-structural carbohydrates into glucose and simple sugars, which are absorbed in the small intestine.

Structural carbohydrates, such as cellulose and hemicellulose in plants, can only be broken down by bacterial enzymes in the cecum and colon. The microorganisms convert these carbohydrates to volatile fatty acids (acetate, propionate, butyrate), which can provide 30 to 70 percent of the horse’s energy requirement.

Fibrous feeds are a very important part of the horse’s diet. They provide nutrients for both the horse and microbes in the hindgut as well as stimulate muscle tone and activity of the gastrointestinal tract.

Mineral supplements are usually required in the horse’s diet. Macrominerals are added to a horse’s diet to balance the ration to meet mineral requirements.

Human raised horses usually have some grazing but get some or much of there food needs from feed. Those feeds often supplement normal food for wild horses with beets, apples, carrots and other sources. In addition the horse food supplements include minerals, fiber and even pre-biotics and pro-biotics (just like our processed food does).

As a general rule, horses need 1 to 2 quarts (2 to 4 liters per kilogram) of water per pound of dry matter consumed. Of course, other factors can increase the water need, such as exercise (since it results in water loss through sweating).

Related: Great Webcast Explaining the Digestive SystemsEnergy Efficiency of DigestionTracking the Ecosystem Within Us

Looking Inside Living Cells

Johns Hopkins’ molecular biologist Jin Zhang explains how she uses light to see where and when within cells specific molecular processes occur and what happens when they go wrong.

Related: How Lysozyme Protein in Our Tear-Drops Kill BacteriaScience Explained: How Cells React to Invading VirusesNobel Prize in Physiology or Medicine 2012 for Reprogramming Cells to be PluripotentWebcast Exploring Eukaryotic Cells

DNA Contains Gene Control Instructions

Scientists discover double meaning in genetic code

Scientists have discovered a second code hiding within DNA. This second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease.

“For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” said Stamatoyannopoulos. “Now we know that this basic assumption about reading the human genome missed half of the picture. These new findings highlight that DNA is an incredibly powerful information storage device, which nature has fully exploited in unexpected ways.”

The genetic code uses a 64-letter alphabet called codons. The UW team discovered that some codons, which they called duons, can have two meanings, one related to protein sequence, and one related to gene control. These two meanings seem to have evolved in concert with each other. The gene control instructions appear to help stabilize certain beneficial features of proteins and how they are made.

The discovery of duons has major implications for how scientists and physicians interpret a patient’s genome and will open new doors to the diagnosis and treatment of disease.

“The fact that the genetic code can simultaneously write two kinds of information means that many DNA changes that appear to alter protein sequences may actually cause disease by disrupting gene control programs or even both mechanisms simultaneously,” said Stamatoyannopoulos.

The wonder of DNA continues to amaze.

Related: Epigenetic Effects on DNA from Living Conditions in Childhood Persist Well Into Middle AgeDNA Passed to Descendants Changed by Your LifeDNA based Algorithmic Self-Assembly

Outdoor Air Pollution Resulted in 223,000 Cancer Deaths in 2010

The specialized cancer agency of the World Health Organization, the International Agency for Research on Cancer (IARC), announced today that it has classified outdoor air pollution as carcinogenic to humans.

After thoroughly reviewing the latest available scientific literature, the world’s leading experts convened by the IARC Monographs Programme concluded that there is sufficient evidence that exposure to outdoor air pollution causes lung cancer. They also noted a positive association with an increased risk of bladder cancer.

Particulate matter, a major component of outdoor air pollution, was evaluated separately and was also classified as carcinogenic to humans.

The IARC evaluation showed an increasing risk of lung cancer with increasing levels of exposure to particulate matter and air pollution. Although the composition of air pollution and levels of exposure can vary dramatically between locations, the conclusions of the Working Group apply to all regions of the world.

Air pollution is already known to increase risks for a wide range of diseases, such as respiratory and heart diseases. Studies indicate that in recent years exposure levels have increased significantly in some parts of the world, particularly in rapidly industrializing countries with large populations. The most recent data indicate that in 2010, 223,000 deaths from lung cancer worldwide resulted from air pollution.

“The air we breathe has become polluted with a mixture of cancer-causing substances,” says Dr Kurt Straif.

The stories of amazingly high (and persistent) air pollution levels in China have been continuing for years. But, while China, likely represents several of the worst existing air pollution conditions hundreds of thousands have died outside China due to air pollution just in the last 5 years.

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Mechanical Gears Found in Jumping Insects

A natural example of a functioning gear mechanism has been discovered in a common insect – the plant-hopper Issus – showing that evolution developed interlocking cogs long before we did.

The gears in the Issus hind-leg bear remarkable engineering resemblance to those found on every bicycle and inside every car gear-box. Each gear tooth has a rounded corner at the point it connects to the gear strip; a feature identical to man-made gears such as bike gears – essentially a shock-absorbing mechanism to stop teeth from shearing off.

The gear teeth on the opposing hind-legs lock together like those in a car gear-box, ensuring almost complete synchronicity in leg movement – the legs always move within 30 ‘microseconds’ of each other, with one microsecond equal to a millionth of a second.

This is critical for the powerful jumps that are this insect’s primary mode of transport, as even miniscule discrepancies in synchronisation between the velocities of its legs at the point of propulsion would result in “yaw rotation” – causing the Issus to spin hopelessly out of control.

“This precise synchronisation would be impossible to achieve through a nervous system, as neural impulses would take far too long for the extraordinarily tight coordination required,” said lead author Professor Malcolm Burrows, from Cambridge’s Department of Zoology.

“By developing mechanical gears, the Issus can just send nerve signals to its muscles to produce roughly the same amount of force – then if one leg starts to propel the jump the gears will interlock, creating absolute synchronicity.

Interestingly, the mechanistic gears are only found in the insect’s juvenile – or ‘nymph’ – stages, and are lost in the final transition to adulthood. These transitions, called ‘molts’, are when animals cast off rigid skin at key points in their development in order to grow.

It may also be down to the larger size of adults and consequently their ‘trochantera’ – the insect equivalent of the femur or thigh bones. The bigger adult trochantera might allow them to can create enough friction to power the enormous leaps from leaf to leaf without the need for intermeshing gear teeth to drive it, say the scientists.

It’s not yet known why the Issus loses its hind-leg gears on reaching adulthood. The scientists point out that a problem with any gear system is that if one tooth on the gear breaks, the effectiveness of the whole mechanism is damaged. While gear-teeth breakage in nymphs could be repaired in the next molt, any damage in adulthood remains permanent. It is amazing what evolution results in, not only gears but a system that changes to a different solution (maybe, who knows the real “reason”) when the gears solution lack of robustness would create a problem for survivability.

While there are examples of apparently ornamental cogs in the animal kingdom – such as on the shell of the cog wheel turtle or the back of the wheel bug – gears with a functional role either remain elusive or have been rendered defunct by evolution.

Related: Using Bacteria to Power Microscopic MachinesWebcast of a T-cell Killing a Cancerous CellBuilding A Better Bed Bug Trap Using Bean Leaves

In the video above, Professor Malcolm Burrows talks about finding the bugs that led to the science, and working with artists Elizabeth Hobbs and Emily Tracy and members of the community in the London borough of Hackney to produce the film ‘Waterfolk’.

Full press release

Exercise Reduces Anxiety While Also Promoting the Growth of New Neurons

Exercise reorganizes the brain to be more resilient to stress

These findings potentially resolve a discrepancy in research related to the effect of exercise on the brain — namely that exercise reduces anxiety while also promoting the growth of new neurons in the ventral hippocampus. Because these young neurons are typically more excitable than their more mature counterparts, exercise should result in more anxiety, not less. The Princeton-led researchers, however, found that exercise also strengthens the mechanisms that prevent these brain cells from firing.

From an evolutionary standpoint, the research also shows that the brain can be extremely adaptive and tailor its own processes to an organism’s lifestyle or surroundings, Gould said. A higher likelihood of anxious behavior may have an adaptive advantage for less physically fit creatures. Anxiety often manifests itself in avoidant behavior and avoiding potentially dangerous situations would increase the likelihood of survival, particularly for those less capable of responding with a “fight or flight” reaction, she said.

The anxiety-reducing effect of exercise was canceled out when the researchers blocked the GABA receptor that calms neuron activity in the ventral hippocampus.

Interesting research (with mice) that explores how exercise makes us more resilient to stress. I know for me, exercise seems to help relieve stress.

Related: Feed your Newborn NeuronsNew Neurons are Needed for New MemoriesRegular Aerobic Exercise for a Faster Brain (2007)Inactivity Leads to 5.3 Million Early Deaths a YearHow Aerobic Exercise Suppresses Appetite

Europe Bans Certain Pesticides, USA Just Keeps Looking, Bees Keep Dying

For years the bee colony collapse disorder has been showing the difficulty of the scientific inquiry process. And that difficulty often becomes more difficult if interests with lots of money at stake want to block certain conclusions.

One-Third of U.S. Honeybee Colonies Died Last Winter, Threatening Food Supply

Multiple factors — pesticides, fungicides, parasites, viruses and malnutrition — are believed to cause the losses, which were officially announced today by a consortium of academic researchers, beekeepers and Department of Agriculture scientists.

“We’re getting closer and closer to the point where we don’t have enough bees in this country to meet pollination demands,” said entomologist Dennis vanEngelstorp of the University of Maryland, who led the survey documenting the declines.

Beekeepers lost 31 percent of their colonies in late 2012 and early 2013, roughly double what’s considered acceptable attrition through natural causes. The losses are in keeping with rates documented since 2006, when beekeeper concerns prompted the first nationwide survey of honeybee health. Hopes raised by drop in rates of loss to 22 percent in 2011-2012 were wiped out by the new numbers.

Most losses reported in the latest survey, however, don’t actually fit the CCD profile. And though CCD is largely undocumented in western Europe, honeybee losses there have also been dramatic. In fact, CCD seems to be declining, even as total losses mount. The honeybees are simply dying.

“Even if CCD went away, we’d still have tremendous losses,” said entomologist Diana Cox-Foster at Pennsylvania State University. “CCD losses are like the straw that breaks the camel’s back. The system has many other issues.”

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Cell Aging and Limits Due to Telomeres

When cells divide the process fails to copy DNA all the way to the end. Telomeres are are the end of DNA strands, as essentially a buffer of material that won’t cause information to be lost when part of the telomere isn’t copied. As DNA is copied, as new cells are created, the length of telomeres at the end is reduced. Once the telomeres are gone the cell will no longer divide.

The 2009 Nobel Prize in Physiology or Medicine went to 3 scientists for discovering how the chromosomes can be copied in a complete way during cell divisions and how they are protected against degradation. The Nobel Laureates have shown that the solution is to be found in the ends of the chromosomes – the telomeres – and in an enzyme that forms them – telomerase.

There is some debate over the benefit of the mechanism of cells not dividing do to lack of telomere. This can prevent cancerous cells from replicating (once they replicate to the extent that the necessary telomere buffer is gone). It is also seen that as telomeres get shorter the cells become more likely to become cancerous.

Cancer also can stimulate the production of telomerase which can stop telomeres from getting shorter as cells divide and thus allow the cancer cells to keep dividing (thus producing more cancer cell and increasing the amount of cancerous cells). Using telomerase to allow health cells to avoid the limits of division is being researched.

Are Telomeres the Key to Aging and Cancer? (University of Utah)

An enzyme named telomerase adds bases to the ends of telomeres. In young cells, telomerase keeps telomeres from wearing down too much. But as cells divide repeatedly, there is not enough telomerase, so the telomeres grow shorter and the cells age.

Cells normally can divide only about 50 to 70 times, with telomeres getting progressively shorter until the cells become senescent, die or sustain genetic damage that can cause cancer.

shorter telomeres are associated with shorter lives. Among people older than 60, those with shorter telomeres were three times more likely to die from heart disease and eight times more likely to die from infectious disease.

While telomere shortening has been linked to the aging process, it is not yet known whether shorter telomeres are just a sign of aging – like gray hair – or actually contribute to aging.

Related: The Naked Mole Rat is the Only Known Cancerless AnimalWebcast of a T-cell Killing a Cancerous CellRNA interference webcast

Huge Human Population Boom 40,000 to 50,000 Years Ago

Interesting open access paper on looking at the Y-chromosome to explore our ancestry: A calibrated human Y-chromosomal phylogeny based on resequencing. I can’t understand all the details but the basic idea isn’t that complicated. It is interesting to see these details as are the conclusions that can be drawn: that we had a big explosion of human population o 41,000–52,000 years ago.

This population explosion occurred, between the first expansion of modern humans out of Africa 60,000 to 70,000 years ago and the Neolithic expansions of people in several parts of the world starting 10,000 years ago.

“We think this second, previously unknown population boom, may have occurred as humans adapted to their new environment after the first out-of-Africa expansion,” says Dr Qasim Ayub, lead author from the Wellcome Trust Sanger institute. “We think that when humans moved from the horn of Africa to Asia, Australia and eventually Europe, they remained in small groups by the coasts. It took them tens of thousands of years to adapt to the mountainous, forested surroundings on the inner continents. However, once their genetic makeup was suited to these new environments, the population increased extremely rapidly as the groups travelled inland and took advantage of the abundance of space and food.”

The work highlights how it is now possible to obtain new biological insights from existing DNA sequencing data sets, and the value of sharing data. The majority of the DNA information used for this study was obtained from freely-available online data-sets.

This is the first time researchers have used the information from large-scale DNA sequencing to create an accurate family tree of the Y chromosome, from which the inferences about human population history could be made.

Full press release

Related: Laser Tool Creates “blueprints” of Archeology SitesHHMI on Science 2.0: Information RevolutionScientists crack 40-year-old DNA puzzle

CDC Again Stresses Urgent Need to Adjust Practices or Pay a Steep Price

Untreatable and hard-to-treat infections from Carbapenem-resistant Enterobacteriaceae (CRE) germs are on the rise among patients in medical facilities. CRE germs have become resistant to all or nearly all the antibiotics we have today. Types of CRE include Klebsiella pneumoniae Carbapenemase (KPC) and New Delhi metallo-beta-lactamase (NDM). By following the United States Center for Disease Control (CDC) guidelines, we can slow the penetration of CRE infections in hospitals and other medical facilities and potentially spread to otherwise healthy people outside of medical facilities.

The CDC has worked with hospitals to successfully apply these measures. The CDC worked with Florida to stop a year-long CRE outbreak in a long-term acute care hospital. With the improved use of CDC recommendations (such as educating staff; dedicating staff, rooms, and equipment to patients with CRE; and improving use of gloves and gowns) the percentage of patients who got CRE at the facility dropped from 44% to 0.

One travesty has been how poorly health care professionals have been about prescribe antibiotics wisely We need to improve and follow CDC antibiotics guidelines (stop the overuse of antibiotics) and use culture results (for patients undergoing treatment) to modify prescriptions, if needed. Antibiotic overuse contributes to the growing problems of Clostridium difficile (c-diff) infection and antibiotic resistance in healthcare facilities. Studies indicate that nearly 50% of antimicrobial use in hospitals is unnecessary or inappropriate (per CDC web site).

Israel decreased CRE infection rates in all 27 of its hospitals by more than 70% in one year with a coordinated prevention program. The USA is at a critical time in which CRE infections could be controlled if addressed in a rapid, coordinated, and consistent effort by doctors, nurses, lab staff, medical facility leadership, health departments/states, policy makers, and the federal government.

As I have been saying for years the damage we are creating due to our actions around the use and abuse of antibiotics is likely to kill tens of thousands, or more people. Because the deaths are delayed and often not dramatic we have continued dangerous practices for years when we know better. It is a shame we are condemning so many to increased risks. The CDC, and others, are doing good work, unfortunately too much bad work is continuing in the face of evidence of how dangerous that is.

Related: CDC Urges Increased Effort to Reduce Drug-Resistant Infections (2006)Key scientific articles on Healthcare Associated Infections via CDCOur Dangerous Antibiotic Practices Carry Great RisksDangerous Drug-Resistant Strains of TB are a Growing Threat

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